
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
import shutil
import os
from tempfile import TemporaryDirectory

use_tempdir = True
if use_tempdir:
    # Create temporary directory
    data_dir = TemporaryDirectory()
    # Save original directory
    orig_dir = os.getcwd()
    # Move to new directory
    os.chdir(data_dir.name)

# For info, print out where the script is running
print("Running in {}".format(os.getcwd()))

Running in /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04


import os
if 'CRDS_CACHE_TYPE' in os.environ:
    if os.environ['CRDS_CACHE_TYPE'] == 'local':
        os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
    elif os.path.isdir(os.environ['CRDS_CACHE_TYPE']):
        os.environ['CRDS_PATH'] = os.environ['CRDS_CACHE_TYPE']
print('CRDS cache location: {}'.format(os.environ['CRDS_PATH']))

CRDS cache location: /grp/crds/cache


import warnings
import psutil
from astropy.io import fits

# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
    warnings.simplefilter("once", category=DeprecationWarning)
    import jwst
    from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
    from jwst.pipeline.calwebb_spec2 import Spec2Pipeline
    from jwst.assign_wcs.assign_wcs_step import AssignWcsStep
    from jwst.msaflagopen.msaflagopen_step import MSAFlagOpenStep
    from jwst.extract_2d.extract_2d_step import Extract2dStep
    from jwst.srctype.srctype_step import SourceTypeStep
    from jwst.wavecorr.wavecorr_step import WavecorrStep
    from jwst.flatfield.flat_field_step import FlatFieldStep

# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml

# import NPTT
import nirspec_pipe_testing_tool as nptt

# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata


# Print versions used for the pipeline and NPTT

pipeline_version = jwst.__version__
nptt_version = nptt.__version__

print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)

Using jwst pipeline version:  1.8.2
Using NPTT version:  2.0.1


testing_data = {

                'mos_g140m_f100lp':{
                                  'uncal_file_nrs1': 'mos_g140m_line1_NRS1_uncal.fits',
                                  'uncal_file_nrs2': 'mos_g140m_line1_NRS2_uncal.fits',  
                                  'sflat_nrs1': 'nirspec_MOS_sflat_G140M_OPAQUE_FLAT1_nrs1_f_01.01.fits',
                                  'sflat_nrs2': 'nirspec_MOS_sflat_G140M_OPAQUE_FLAT1_nrs2_f_01.01.fits',
                                  'fflat': 'nirspec_MOS_fflat_F100LP_01.01.fits',
                                  'msa_shutter_config': 'V8460001000101_msa.fits' }

                }


# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
    """This function creates a list with all the files needed per detector to run the test.
    Args:
        data_set_dict: dictionary, contains inputs for a specific mode and configuration
        detector: string, either nrs1 or nrs2
    Returns:
        data: list, contains all files needed to run test
    """
    files2obtain = ['uncal_file_nrs1', 'sflat_nrs1', 'fflat', 'msa_shutter_config']
    data = []
    for file in files2obtain:
        data_file = None
        try: 
            if '_nrs' in file and '2' in detector:
                file = file.replace('_nrs1', '_nrs2')

            data_file = get_bigdata('jwst_validation_notebooks',
                                         'validation_data',
                                         'nirspec_data', 
                                         data_set_dict[file])
        except TypeError:
            data.append(None)
            continue

        data.append(data_file)

    return data


# set the D-flat path (used for all test data)
print('Getting D-Flats from Artifactory...')

dflat_nrs1 = get_bigdata('jwst_validation_notebooks',
                         'validation_data',
                         'nirspec_data', 
                         'nirspec_dflat_nrs1_f_01.03.fits')

dflat_nrs2 = get_bigdata('jwst_validation_notebooks',
                         'validation_data',
                         'nirspec_data', 
                         'nirspec_dflat_nrs2_f_01.03.fits')
print('Got D-flats')

# set NPTT switches for this test and other variables
writefile = False
save_figs = False
show_figs = True
results_dict = {}
detectors = ['nrs1', 'nrs2']

Getting D-Flats from Artifactory...
Got D-flats


# Get data for MOS

for mode_config, data_set_dict in testing_data.items():
    if 'mos' not in mode_config:
        continue
        
    print('Starting to run pipeline and test for mode: ', mode_config)
    
    for detector in detectors:
        print('Testing files for detector: ', detector)
        data = get_artifactory_file(data_set_dict, detector)
        uncal_file, sflat, fflat, msa_shutter_config = data
        print('Working with uncal_file: ', uncal_file)
        uncal_basename = os.path.basename(uncal_file)
        dflat = dflat_nrs1
        if '2' in detector:
            dflat = dflat_nrs2
        
        # Make sure these keywords are properly set
        filt = fits.getval(uncal_file, 'FILTER')
        if 'OPAQUE' in filt or 'allslits' in uncal_basename.lower():
            if 'clear' in uncal_basename.lower():
                filt = 'CLEAR'
            else:
                l = uncal_basename.split("_")
                for li in l:
                    if 'lp' in li.lower():
                        filt = li
                        break
            fits.setval(uncal_file, 'FILTER', value=filt)
        print('Filter = ', filt)

        # Run the stage 1 pipeline 
        print('Running the detector1 pipeline...')
        rate_object = Detector1Pipeline.call(uncal_file)
        
        # Make sure the MSA shutter configuration file is set up correctly
        if msa_shutter_config is not None:
            msa_metadata = rate_object.meta.instrument.msa_metadata_file
            if msa_metadata is None or msa_metadata == 'N/A':
                rate_object.meta.instrument.msa_metadata_file = msa_shutter_config

        # Make sure the FXD_SLIT keyword is set correctly
        try:
            if 'full' in rate_object.meta.instrument.fixed_slit:
                rate_object.meta.instrument.fixed_slit = 'NONE'
        except TypeError:
            print('FXD_SLIT keyword = ', rate_object.meta.instrument.fixed_slit)
        
        # Run the stage 2 pipeline steps
        print('\nRunning the spec2 pipeline...')
        skip_file = False
        try:
            parameter_dict = {"flat_field": {"save_interpolated_flat": True},
                              "pathloss": {"skip": True},
                              "barshadow": {"skip": True},
                              "photom": {"skip": True},
                              "resample_spec": {"skip": True},
                              "cube_build": {"skip": True},
                              "extract_1d": {"skip": True}
                             }
            flat_field_object = Spec2Pipeline.call(rate_object, steps=parameter_dict)
        except:
            #print("No open slits fall on detector ", det)  # usually why assign_wcs crashes
            print("* Spec2 pipeline CRASHED or exited with no output for detector ", detector)
            print("  Skipping test for this file. \n")
            skip_file = True
            
        if not skip_file:   
            # accepted threshold difference with respect to benchmark files
            threshold_diff = 9.999e-5
            if 'prism' in uncal_basename.lower():
                threshold_diff = 9.999e-3
            
            # Run the validation test
            %matplotlib inline
            interpolated_flat = os.path.basename(uncal_file).replace('uncal', 'interpolatedflat')
            print('Running flat field test for MOS...')
            result, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.flattest_mos.flattest(
                                                                            flat_field_object,
                                                                            dflat_path=dflat,
                                                                            sflat_path=sflat, 
                                                                            fflat_path=fflat,
                                                                            msa_shutter_conf=msa_shutter_config,     
                                                                            writefile=writefile,
                                                                            show_figs=show_figs, 
                                                                            save_figs=save_figs,
                                                                            interpolated_flat=interpolated_flat,
                                                                            threshold_diff=threshold_diff,
                                                                            debug=False)
        else:
            result, result_msg = 'skipped', 'skipped'

        # Did the test passed 
        print("Did flat_field for ", mode_config, " validation test passed? ", result_msg, "\n\n")
        rd = {uncal_basename: result}
        results_dict.update(rd)
        
        # close all open files
        psutil.Process().open_files()
        closing_files = []
        for fd in psutil.Process().open_files():
            if data_dir.name in fd.path:
                closing_files.append(fd)
        for fd in closing_files:
            try:
                print('Closing file: ', fd, '\n\n')
                open(fd.fd).close()
            except:
                print('File already closed: ', fd, '\n\n')

Starting to run pipeline and test for mode:  mos_g140m_f100lp
Testing files for detector:  nrs1
Working with uncal_file:  /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04/mos_g140m_line1_NRS1_uncal.fits
Filter =  F100LP
Running the detector1 pipeline...

2022-12-03 22:58:04,531 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2022-12-03 22:58:04,558 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2022-12-03 22:58:04,560 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2022-12-03 22:58:04,562 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2022-12-03 22:58:04,563 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2022-12-03 22:58:04,564 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2022-12-03 22:58:04,566 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2022-12-03 22:58:04,568 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2022-12-03 22:58:04,569 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2022-12-03 22:58:04,570 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2022-12-03 22:58:04,571 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2022-12-03 22:58:04,573 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2022-12-03 22:58:04,574 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2022-12-03 22:58:04,576 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2022-12-03 22:58:04,577 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2022-12-03 22:58:04,580 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2022-12-03 22:58:04,582 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2022-12-03 22:58:04,584 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2022-12-03 22:58:04,821 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04/mos_g140m_line1_NRS1_uncal.fits',).
2022-12-03 22:58:04,831 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'n_pix_grow_sat': 1}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2022-12-03 22:58:05,022 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'mos_g140m_line1_NRS1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2022-12-03 22:58:05,048 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits'.
2022-12-03 22:58:05,050 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2022-12-03 22:58:05,051 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits'.
2022-12-03 22:58:05,054 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits'.
2022-12-03 22:58:05,055 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2022-12-03 22:58:05,056 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits'.
2022-12-03 22:58:05,057 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2022-12-03 22:58:05,058 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2022-12-03 22:58:05,058 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2022-12-03 22:58:05,058 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits'.
2022-12-03 22:58:05,060 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits'.
2022-12-03 22:58:05,062 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2022-12-03 22:58:05,063 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2022-12-03 22:58:05,063 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2022-12-03 22:58:05,576 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:05,578 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04'}
2022-12-03 22:58:05,714 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2022-12-03 22:58:05,715 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2022-12-03 22:58:05,718 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2022-12-03 22:58:05,965 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:05,967 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04'}
2022-12-03 22:58:05,994 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits
2022-12-03 22:58:06,993 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2022-12-03 22:58:07,237 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:07,239 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04', 'n_pix_grow_sat': 1}
2022-12-03 22:58:07,264 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0023.fits
2022-12-03 22:58:10,614 - stpipe.Detector1Pipeline.saturation - INFO - Detected 108240 saturated pixels
2022-12-03 22:58:10,641 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2022-12-03 22:58:10,655 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2022-12-03 22:58:10,906 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:10,908 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04'}
2022-12-03 22:58:10,908 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2022-12-03 22:58:10,912 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2022-12-03 22:58:11,150 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:11,152 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04'}
2022-12-03 22:58:11,178 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits
2022-12-03 22:58:15,096 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2022-12-03 22:58:15,344 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:15,346 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2022-12-03 22:58:15,473 - stpipe.Detector1Pipeline.refpix - INFO - NIR full frame data
2022-12-03 22:58:15,475 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are valid for this mode:
2022-12-03 22:58:15,475 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2022-12-03 22:58:15,476 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2022-12-03 22:58:15,476 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2022-12-03 22:58:15,477 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2022-12-03 22:58:15,477 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is not applicable and is ignored:
2022-12-03 22:58:15,478 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2022-12-03 22:58:18,586 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2022-12-03 22:58:18,736 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:18,737 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04'}
2022-12-03 22:58:18,781 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0019.fits
2022-12-03 22:58:26,990 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2022-12-03 22:58:27,108 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:27,109 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04', 'dark_output': None}
2022-12-03 22:58:27,134 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits
2022-12-03 22:58:33,427 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=6, nframes=1, groupgap=0
2022-12-03 22:58:33,428 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2022-12-03 22:58:33,717 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2022-12-03 22:58:33,833 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:33,835 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}
2022-12-03 22:58:33,845 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2022-12-03 22:58:33,865 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-03 22:58:33,944 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2022-12-03 22:58:35,912 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2022-12-03 22:58:35,978 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/twopoint_difference.py:154: RuntimeWarning: All-NaN slice encountered
  max_ratio = np.nanmax(ratio, axis=0)
2022-12-03 22:58:38,202 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 41569 pixels with at least one CR from five or more groups.
2022-12-03 22:58:44,934 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 9.02095 sec
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:302: RuntimeWarning: invalid value encountered in divide
  data /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:303: RuntimeWarning: invalid value encountered in divide
  err /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:304: RuntimeWarning: invalid value encountered in divide
  readnoise_2d /= gain_2d
2022-12-03 22:58:45,044 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 11.199386
2022-12-03 22:58:45,050 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2022-12-03 22:58:45,164 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 6, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:58:45,166 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}
2022-12-03 22:58:45,204 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2022-12-03 22:58:45,205 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-03 22:58:45,326 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2022-12-03 22:58:45,326 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/ramp_fitting/ols_fit.py:1089: RuntimeWarning: invalid value encountered in multiply
  var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2022-12-03 22:59:10,853 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 6
2022-12-03 22:59:10,854 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2022-12-03 22:59:11,027 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2022-12-03 22:59:11,163 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:11,165 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04'}
2022-12-03 22:59:11,236 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-03 22:59:11,237 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-03 22:59:11,241 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-03 22:59:11,343 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:11,345 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04'}
2022-12-03 22:59:11,418 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-03 22:59:11,419 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-03 22:59:11,423 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-03 22:59:11,424 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2022-12-03 22:59:11,424 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-03 22:59:11,424 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2022-12-03 22:59:11,450 - CRDS - ERROR -  Error determining best reference for 'pars-residualfringestep'  =   Unknown reference type 'pars-residualfringestep'
2022-12-03 22:59:11,467 - stpipe.Spec2Pipeline - INFO - Spec2Pipeline instance created.
2022-12-03 22:59:11,468 - stpipe.Spec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created.
2022-12-03 22:59:11,470 - stpipe.Spec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created.
2022-12-03 22:59:11,470 - stpipe.Spec2Pipeline.imprint_subtract - INFO - ImprintStep instance created.
2022-12-03 22:59:11,471 - stpipe.Spec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created.
2022-12-03 22:59:11,473 - stpipe.Spec2Pipeline.extract_2d - INFO - Extract2dStep instance created.
2022-12-03 22:59:11,475 - stpipe.Spec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created.
2022-12-03 22:59:11,476 - stpipe.Spec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created.
2022-12-03 22:59:11,477 - stpipe.Spec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created.
2022-12-03 22:59:11,478 - stpipe.Spec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created.
2022-12-03 22:59:11,479 - stpipe.Spec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created.
2022-12-03 22:59:11,480 - stpipe.Spec2Pipeline.wavecorr - INFO - WavecorrStep instance created.
2022-12-03 22:59:11,481 - stpipe.Spec2Pipeline.flat_field - INFO - FlatFieldStep instance created.
2022-12-03 22:59:11,482 - stpipe.Spec2Pipeline.srctype - INFO - SourceTypeStep instance created.
2022-12-03 22:59:11,483 - stpipe.Spec2Pipeline.straylight - INFO - StraylightStep instance created.
2022-12-03 22:59:11,484 - stpipe.Spec2Pipeline.fringe - INFO - FringeStep instance created.
2022-12-03 22:59:11,485 - stpipe.Spec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created.
2022-12-03 22:59:11,486 - stpipe.Spec2Pipeline.pathloss - INFO - PathLossStep instance created.
2022-12-03 22:59:11,487 - stpipe.Spec2Pipeline.barshadow - INFO - BarShadowStep instance created.
2022-12-03 22:59:11,488 - stpipe.Spec2Pipeline.wfss_contam - INFO - WfssContamStep instance created.
2022-12-03 22:59:11,489 - stpipe.Spec2Pipeline.photom - INFO - PhotomStep instance created.
2022-12-03 22:59:11,490 - stpipe.Spec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created.
2022-12-03 22:59:11,492 - stpipe.Spec2Pipeline.cube_build - INFO - CubeBuildStep instance created.
2022-12-03 22:59:11,493 - stpipe.Spec2Pipeline.extract_1d - INFO - Extract1dStep instance created.
2022-12-03 22:59:11,600 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:11,615 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_bsub': False, 'fail_on_exception': True, 'save_wfss_esec': False, 'steps': {'bkg_subtract': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_combined_background': False, 'sigma': 3.0, 'maxiters': None, 'wfss_mmag_extract': None}, 'assign_wcs': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.55, 'slit_y_high': 0.55}, 'imprint_subtract': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'msa_flagging': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'extract_2d': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'grism_objects': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'wfss_mmag_extract': None, 'wfss_nbright': 1000}, 'master_background_mos': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'force_subtract': False, 'save_background': False, 'user_background': None, 'inverse': False, 'steps': {'flat_field': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}, 'pathloss': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'barshadow': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'photom': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}}}, 'wavecorr': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'flat_field': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': True, 'user_supplied_flat': None, 'inverse': False}, 'srctype': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'source_type': None}, 'straylight': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'fringe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'residual_fringe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': 'residual_fringe', 'search_output_file': False, 'input_dir': '', 'save_intermediate_results': False, 'ignore_region_min': None, 'ignore_region_max': None}, 'pathloss': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'barshadow': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'wfss_contam': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_simulated_image': False, 'save_contam_images': False, 'maximum_cores': 'none'}, 'photom': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'resample_spec': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'pixfrac': 1.0, 'kernel': 'square', 'fillval': 'INDEF', 'weight_type': 'ivm', 'output_shape': None, 'crpix': None, 'crval': None, 'rotation': None, 'pixel_scale_ratio': 1.0, 'pixel_scale': None, 'single': False, 'blendheaders': True, 'allowed_memory': None, 'in_memory': True}, 'cube_build': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': False, 'input_dir': '', 'channel': 'all', 'band': 'all', 'grating': 'all', 'filter': 'all', 'output_type': 'band', 'scale1': 0.0, 'scale2': 0.0, 'scalew': 0.0, 'weighting': 'drizzle', 'coord_system': 'skyalign', 'rois': 0.0, 'roiw': 0.0, 'weight_power': 2.0, 'wavemin': None, 'wavemax': None, 'single': False, 'skip_dqflagging': False}, 'extract_1d': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'smoothing_length': None, 'bkg_fit': None, 'bkg_order': None, 'bkg_sigma_clip': 3.0, 'log_increment': 50, 'subtract_background': None, 'use_source_posn': None, 'center_xy': None, 'apply_apcorr': True, 'soss_threshold': 0.01, 'soss_n_os': 2, 'soss_transform': None, 'soss_tikfac': None, 'soss_width': 40.0, 'soss_bad_pix': 'model', 'soss_modelname': None}}}
2022-12-03 22:59:11,622 - stpipe.Spec2Pipeline - INFO - Prefetching reference files for dataset: 'mos_g140m_line1_NRS1_uncal.fits' reftypes = ['camera', 'collimator', 'dflat', 'disperser', 'distortion', 'fflat', 'filteroffset', 'flat', 'fore', 'fpa', 'fringe', 'ifufore', 'ifupost', 'ifuslicer', 'mrsxartcorr', 'msa', 'msaoper', 'ote', 'regions', 'sflat', 'specwcs', 'wavecorr', 'wavelengthrange', 'wfssbkg']

Running the spec2 pipeline...

2022-12-03 22:59:11,669 - stpipe.Spec2Pipeline - INFO - Prefetch for CAMERA reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf'.
2022-12-03 22:59:11,674 - stpipe.Spec2Pipeline - INFO - Prefetch for COLLIMATOR reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf'.
2022-12-03 22:59:11,676 - stpipe.Spec2Pipeline - INFO - Prefetch for DFLAT reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dflat_0001.fits'.
2022-12-03 22:59:11,678 - stpipe.Spec2Pipeline - INFO - Prefetch for DISPERSER reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf'.
2022-12-03 22:59:11,680 - stpipe.Spec2Pipeline - INFO - Prefetch for DISTORTION reference file is 'N/A'.
2022-12-03 22:59:11,680 - stpipe.Spec2Pipeline - INFO - Prefetch for FFLAT reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_fflat_0018.fits'.
2022-12-03 22:59:11,682 - stpipe.Spec2Pipeline - INFO - Prefetch for FILTEROFFSET reference file is 'N/A'.
2022-12-03 22:59:11,682 - stpipe.Spec2Pipeline - INFO - Prefetch for FLAT reference file is 'N/A'.
2022-12-03 22:59:11,683 - stpipe.Spec2Pipeline - INFO - Prefetch for FORE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf'.
2022-12-03 22:59:11,684 - stpipe.Spec2Pipeline - INFO - Prefetch for FPA reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf'.
2022-12-03 22:59:11,689 - stpipe.Spec2Pipeline - INFO - Prefetch for FRINGE reference file is 'N/A'.
2022-12-03 22:59:11,690 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUFORE reference file is 'N/A'.
2022-12-03 22:59:11,690 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUPOST reference file is 'N/A'.
2022-12-03 22:59:11,690 - stpipe.Spec2Pipeline - INFO - Prefetch for IFUSLICER reference file is 'N/A'.
2022-12-03 22:59:11,691 - stpipe.Spec2Pipeline - INFO - Prefetch for MRSXARTCORR reference file is 'N/A'.
2022-12-03 22:59:11,691 - stpipe.Spec2Pipeline - INFO - Prefetch for MSA reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf'.
2022-12-03 22:59:11,693 - stpipe.Spec2Pipeline - INFO - Prefetch for MSAOPER reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json'.
2022-12-03 22:59:11,695 - stpipe.Spec2Pipeline - INFO - Prefetch for OTE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf'.
2022-12-03 22:59:11,697 - stpipe.Spec2Pipeline - INFO - Prefetch for REGIONS reference file is 'N/A'.
2022-12-03 22:59:11,697 - stpipe.Spec2Pipeline - INFO - Prefetch for SFLAT reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_sflat_0003.fits'.
2022-12-03 22:59:11,699 - stpipe.Spec2Pipeline - INFO - Prefetch for SPECWCS reference file is 'N/A'.
2022-12-03 22:59:11,699 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVECORR reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0004.asdf'.
2022-12-03 22:59:11,701 - stpipe.Spec2Pipeline - INFO - Prefetch for WAVELENGTHRANGE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf'.
2022-12-03 22:59:11,702 - stpipe.Spec2Pipeline - INFO - Prefetch for WFSSBKG reference file is 'N/A'.
2022-12-03 22:59:11,702 - stpipe.Spec2Pipeline - INFO - Starting calwebb_spec2 ...
2022-12-03 22:59:11,760 - stpipe.Spec2Pipeline - INFO - Processing product mos_g140m_line1_NRS1_uncal
2022-12-03 22:59:11,760 - stpipe.Spec2Pipeline - INFO - Working on input <ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits> ...
2022-12-03 22:59:11,878 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:11,880 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2022-12-03 22:59:12,032 - stpipe.Spec2Pipeline.assign_wcs - INFO - Retrieving open MSA slitlets for msa_metadata_id = 1 and dither_index = 1
2022-12-03 22:59:12,257 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1260581910610199 deg
2022-12-03 22:59:12,258 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3316612243652344 deg
2022-12-03 22:59:12,259 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.0002496099796717191 deg
2022-12-03 22:59:12,260 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0 deg
2022-12-03 22:59:12,545 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 6 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,558 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 7 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,570 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 8 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,583 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 9 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,596 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 10 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,608 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 11 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,621 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 14 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,633 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 15 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,645 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 16 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,658 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 17 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,671 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 18 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,683 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 19 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,695 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 21 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,707 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 25 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,720 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 26 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,732 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 27 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,746 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 29 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,759 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 31 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,771 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 32 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,783 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 33 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,795 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 35 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,809 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 37 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,821 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 38 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,833 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 39 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,845 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 41 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,880 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 1 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,893 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 2 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,905 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 3 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,917 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 4 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,929 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 5 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,941 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 12 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,954 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 13 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,966 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 20 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,978 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 22 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:12,990 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 23 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:13,002 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 24 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:13,015 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 28 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:13,027 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 30 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:13,039 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 34 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:13,051 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 36 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:13,063 - stpipe.Spec2Pipeline.assign_wcs - INFO - Removing slit 40 from the list of open slits because the WCS bounding_box is completely outside the detector.
2022-12-03 22:59:13,353 - stpipe.Spec2Pipeline.assign_wcs - INFO - Slits projected on detector NRS1: [42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]
2022-12-03 22:59:13,353 - stpipe.Spec2Pipeline.assign_wcs - INFO - Computing WCS for 27 open slitlets
2022-12-03 22:59:13,389 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_ytilt is 0.1260581910610199 deg
2022-12-03 22:59:13,389 - stpipe.Spec2Pipeline.assign_wcs - INFO - gwa_xtilt is 0.3316612243652344 deg
2022-12-03 22:59:13,390 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_y correction: 0.0002496099796717191 deg
2022-12-03 22:59:13,391 - stpipe.Spec2Pipeline.assign_wcs - INFO - theta_x correction: 0.0 deg
2022-12-03 22:59:13,407 - stpipe.Spec2Pipeline.assign_wcs - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2022-12-03 22:59:13,557 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 2 open slits in quadrant 1
2022-12-03 22:59:13,573 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 11 open slits in quadrant 2
2022-12-03 22:59:13,657 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 4 open slits in quadrant 3
2022-12-03 22:59:13,688 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 10 open slits in quadrant 4
2022-12-03 22:59:13,899 - stpipe.Spec2Pipeline.assign_wcs - INFO - There are 0 open slits in quadrant 5
2022-12-03 22:59:14,069 - stpipe.Spec2Pipeline.assign_wcs - INFO - Created a NIRSPEC nrs_msaspec pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0032.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0023.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': None, 'ifufore': None, 'ifuslicer': None, 'msametafile': 'V8460001000101_msa.fits'}
2022-12-03 22:59:14,942 - stpipe.Spec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2022-12-03 22:59:14,955 - stpipe.Spec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2022-12-03 22:59:15,096 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>, []).
2022-12-03 22:59:15,098 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_combined_background': False, 'sigma': 3.0, 'maxiters': None, 'wfss_mmag_extract': None}
2022-12-03 22:59:15,098 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step skipped.
2022-12-03 22:59:15,101 - stpipe.Spec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2022-12-03 22:59:15,237 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>, []).
2022-12-03 22:59:15,238 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-03 22:59:15,239 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step skipped.
2022-12-03 22:59:15,241 - stpipe.Spec2Pipeline.imprint_subtract - INFO - Step imprint_subtract done
2022-12-03 22:59:15,376 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:15,378 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-03 22:59:15,395 - stpipe.Spec2Pipeline.msa_flagging - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2022-12-03 22:59:15,396 - stpipe.JwstStep - INFO - JwstStep instance created.
2022-12-03 22:59:15,525 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_ytilt is 0.1260581910610199 deg
2022-12-03 22:59:15,526 - stpipe.Spec2Pipeline.msa_flagging - INFO - gwa_xtilt is 0.3316612243652344 deg
2022-12-03 22:59:15,527 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_y correction: 0.0002496099796717191 deg
2022-12-03 22:59:15,528 - stpipe.Spec2Pipeline.msa_flagging - INFO - theta_x correction: 0.0 deg
2022-12-03 22:59:15,542 - stpipe.Spec2Pipeline.msa_flagging - INFO - SPORDER= -1, wrange=[9.7e-07, 1.89e-06]
2022-12-03 22:59:15,690 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 5 open slits in quadrant 1
2022-12-03 22:59:15,727 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 2
2022-12-03 22:59:15,750 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 9 open slits in quadrant 3
2022-12-03 22:59:15,818 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 3 open slits in quadrant 4
2022-12-03 22:59:15,841 - stpipe.Spec2Pipeline.msa_flagging - INFO - There are 0 open slits in quadrant 5
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2324.820049828629.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2244.599990785436.
  warnings.warn(f"Invalid interval: upper bound {upper} "
2022-12-03 22:59:28,950 - stpipe.Spec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2022-12-03 22:59:29,264 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<ImageModel(2048, 2048) from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:29,265 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'grism_objects': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'wfss_mmag_extract': None, 'wfss_nbright': 1000}
2022-12-03 22:59:29,303 - stpipe.Spec2Pipeline.extract_2d - INFO - EXP_TYPE is NRS_MSASPEC
2022-12-03 22:59:29,770 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 53
2022-12-03 22:59:29,772 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1542 2048
2022-12-03 22:59:29,772 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1316 1326
2022-12-03 22:59:29,963 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:29,972 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2022-12-03 22:59:29,973 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.226123221 -45.673642180 156.225994086 -45.673519691 156.225931834 -45.673551545 156.226060967 -45.673674035
2022-12-03 22:59:30,599 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 54
2022-12-03 22:59:30,600 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1542 2048
2022-12-03 22:59:30,600 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1306 1316
2022-12-03 22:59:30,788 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:30,797 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2022-12-03 22:59:30,798 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.225872406 -45.673404272 156.225743296 -45.673281804 156.225681049 -45.673313656 156.225810156 -45.673436124
2022-12-03 22:59:31,433 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 42
2022-12-03 22:59:31,434 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 2018 2048
2022-12-03 22:59:31,434 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 546 555
2022-12-03 22:59:31,621 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:31,629 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2022-12-03 22:59:31,631 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.223646010 -45.647128995 156.223518121 -45.647008321 156.223456024 -45.647039957 156.223583911 -45.647160632
2022-12-03 22:59:32,465 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 43
2022-12-03 22:59:32,466 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1970 2048
2022-12-03 22:59:32,466 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 415 424
2022-12-03 22:59:32,655 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:32,664 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2022-12-03 22:59:32,665 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.218966486 -45.644829601 156.218838959 -45.644709141 156.218776943 -45.644740759 156.218904467 -45.644861220
2022-12-03 22:59:33,119 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 44
2022-12-03 22:59:33,120 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1969 2048
2022-12-03 22:59:33,120 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 405 414
2022-12-03 22:59:33,304 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:33,312 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2022-12-03 22:59:33,313 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.218718991 -45.644595818 156.218591488 -45.644475376 156.218529475 -45.644506992 156.218656977 -45.644627436
2022-12-03 22:59:33,992 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 45
2022-12-03 22:59:33,993 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1908 2048
2022-12-03 22:59:33,993 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 531 541
2022-12-03 22:59:34,179 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:34,188 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2022-12-03 22:59:34,189 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.219673020 -45.648613077 156.219545303 -45.648492383 156.219483265 -45.648524021 156.219610979 -45.648644716
2022-12-03 22:59:34,869 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 46
2022-12-03 22:59:34,869 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1882 2048
2022-12-03 22:59:34,870 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 203 213
2022-12-03 22:59:35,061 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:35,070 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2022-12-03 22:59:35,071 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.211127421 -45.641279813 156.211000463 -45.641159678 156.210938572 -45.641191268 156.211065527 -45.641311404
2022-12-03 22:59:35,531 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 47
2022-12-03 22:59:35,532 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1815 2048
2022-12-03 22:59:35,533 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 567 576
2022-12-03 22:59:35,726 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:35,734 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2022-12-03 22:59:35,736 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.217456055 -45.651006881 156.217328370 -45.650886079 156.217266356 -45.650917729 156.217394038 -45.651038531
2022-12-03 22:59:36,450 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 48
2022-12-03 22:59:36,451 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1815 2048
2022-12-03 22:59:36,451 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 562 571
2022-12-03 22:59:36,640 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:36,649 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2022-12-03 22:59:36,650 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.217332149 -45.650889654 156.217204477 -45.650768862 156.217142464 -45.650800511 156.217270135 -45.650921304
2022-12-03 22:59:37,327 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 49
2022-12-03 22:59:37,327 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1791 2048
2022-12-03 22:59:37,328 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 632 642
2022-12-03 22:59:37,516 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:37,525 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2022-12-03 22:59:37,526 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.218210913 -45.652969013 156.218083107 -45.652848076 156.218021073 -45.652879740 156.218148877 -45.653000678
2022-12-03 22:59:37,983 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 50
2022-12-03 22:59:37,983 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1774 2048
2022-12-03 22:59:37,984 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 239 249
2022-12-03 22:59:38,169 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:38,178 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2022-12-03 22:59:38,179 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.208399869 -45.643929179 156.208272959 -45.643808942 156.208211096 -45.643840541 156.208338005 -45.643960778
2022-12-03 22:59:38,899 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 51
2022-12-03 22:59:38,900 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1759 2048
2022-12-03 22:59:38,900 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 431 441
2022-12-03 22:59:39,089 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:39,098 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2022-12-03 22:59:39,100 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.212403238 -45.648718689 156.212275928 -45.648598111 156.212213993 -45.648629742 156.212341301 -45.648750320
2022-12-03 22:59:39,564 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 52
2022-12-03 22:59:39,565 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1722 2048
2022-12-03 22:59:39,565 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 804 814
2022-12-03 22:59:39,755 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:39,764 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2022-12-03 22:59:39,765 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.219947139 -45.658234585 156.219819020 -45.658113276 156.219756938 -45.658144979 156.219885055 -45.658266289
2022-12-03 22:59:40,495 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 55
2022-12-03 22:59:40,496 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 1022 2048
2022-12-03 22:59:40,496 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1416 1430
2022-12-03 22:59:40,697 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:40,706 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2022-12-03 22:59:40,707 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.211226719 -45.684941334 156.211098073 -45.684818233 156.211035880 -45.684850241 156.211164524 -45.684973343
2022-12-03 22:59:41,412 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 65
2022-12-03 22:59:41,413 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 427 1893
2022-12-03 22:59:41,413 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1252 1273
2022-12-03 22:59:41,618 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:41,627 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.187669449 -45.691221095 156.187541886 -45.691097893 156.187479754 -45.691130071 156.187607315 -45.691253274
2022-12-03 22:59:41,628 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.187669449 -45.691221095 156.187541886 -45.691097893 156.187479754 -45.691130071 156.187607315 -45.691253274
2022-12-03 22:59:42,091 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 66
2022-12-03 22:59:42,092 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 426 1892
2022-12-03 22:59:42,093 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1453 1474
2022-12-03 22:59:42,301 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:42,309 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.192290190 -45.696194513 156.192162195 -45.696070854 156.192099979 -45.696103094 156.192227972 -45.696226755
2022-12-03 22:59:42,310 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.192290190 -45.696194513 156.192162195 -45.696070854 156.192099979 -45.696103094 156.192227972 -45.696226755
2022-12-03 22:59:43,046 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 68
2022-12-03 22:59:43,048 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 375 1842
2022-12-03 22:59:43,048 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 1477 1500
2022-12-03 22:59:43,268 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:43,277 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.191192483 -45.697686513 156.191064493 -45.697562756 156.191002259 -45.697595026 156.191130247 -45.697718784
2022-12-03 22:59:43,279 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.191192483 -45.697686513 156.191064493 -45.697562756 156.191002259 -45.697595026 156.191130247 -45.697718784
2022-12-03 22:59:43,739 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 56
2022-12-03 22:59:43,739 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 872 2048
2022-12-03 22:59:43,740 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 769 783
2022-12-03 22:59:43,932 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:43,941 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2022-12-03 22:59:43,942 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.191122501 -45.671742959 156.190995485 -45.671621176 156.190933579 -45.671653049 156.191060593 -45.671774833
2022-12-03 22:59:44,688 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 57
2022-12-03 22:59:44,689 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 805 2048
2022-12-03 22:59:44,689 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 355 370
2022-12-03 22:59:44,887 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:44,896 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2022-12-03 22:59:44,898 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.179343124 -45.662963603 156.179216994 -45.662842617 156.179155236 -45.662874401 156.179281365 -45.662995389
2022-12-03 22:59:45,373 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 58
2022-12-03 22:59:45,374 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 731 2048
2022-12-03 22:59:45,374 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 259 275
2022-12-03 22:59:45,569 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:45,578 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.174716949 -45.661919476 156.174591057 -45.661798624 156.174529324 -45.661830406 156.174655215 -45.661951259
2022-12-03 22:59:45,580 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.174716949 -45.661919476 156.174591057 -45.661798624 156.174529324 -45.661830406 156.174655215 -45.661951259
2022-12-03 22:59:46,366 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 59
2022-12-03 22:59:46,367 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 658 2048
2022-12-03 22:59:46,367 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 72 88
2022-12-03 22:59:46,563 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:46,573 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.167987333 -45.658726530 156.167861814 -45.658605973 156.167800128 -45.658637729 156.167925645 -45.658758288
2022-12-03 22:59:46,574 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.167987333 -45.658726530 156.167861814 -45.658605973 156.167800128 -45.658637729 156.167925645 -45.658758288
2022-12-03 22:59:47,038 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 60
2022-12-03 22:59:47,039 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 641 2048
2022-12-03 22:59:47,039 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 682 699
2022-12-03 22:59:47,283 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:47,292 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.181507045 -45.673611447 156.181380443 -45.673489678 156.181318559 -45.673521602 156.181445158 -45.673643373
2022-12-03 22:59:47,293 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.181507045 -45.673611447 156.181380443 -45.673489678 156.181318559 -45.673521602 156.181445158 -45.673643373
2022-12-03 22:59:48,070 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 61
2022-12-03 22:59:48,071 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 620 2048
2022-12-03 22:59:48,071 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 823 840
2022-12-03 22:59:48,272 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:48,281 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.184095390 -45.677365774 156.183968526 -45.677243686 156.183906587 -45.677275659 156.184033450 -45.677397747
2022-12-03 22:59:48,282 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.184095390 -45.677365774 156.183968526 -45.677243686 156.183906587 -45.677275659 156.184033450 -45.677397747
2022-12-03 22:59:48,741 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 62
2022-12-03 22:59:48,742 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 570 2032
2022-12-03 22:59:48,742 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 510 528
2022-12-03 22:59:48,940 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:48,949 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.175200333 -45.670700849 156.175074128 -45.670579384 156.175012293 -45.670611285 156.175138497 -45.670732752
2022-12-03 22:59:48,950 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.175200333 -45.670700849 156.175074128 -45.670579384 156.175012293 -45.670611285 156.175138497 -45.670732752
2022-12-03 22:59:49,757 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 63
2022-12-03 22:59:49,758 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 454 1915
2022-12-03 22:59:49,759 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 182 200
2022-12-03 22:59:49,977 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:49,986 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.163846800 -45.664818400 156.163721256 -45.664697497 156.163659498 -45.664729348 156.163785040 -45.664850252
2022-12-03 22:59:49,987 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.163846800 -45.664818400 156.163721256 -45.664697497 156.163659498 -45.664729348 156.163785040 -45.664850252
2022-12-03 22:59:50,446 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 64
2022-12-03 22:59:50,447 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 454 1915
2022-12-03 22:59:50,447 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 177 195
2022-12-03 22:59:50,687 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:50,695 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.163724974 -45.664701077 156.163599439 -45.664580184 156.163537682 -45.664612033 156.163663216 -45.664732928
2022-12-03 22:59:50,697 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.163724974 -45.664701077 156.163599439 -45.664580184 156.163537682 -45.664612033 156.163663216 -45.664732928
2022-12-03 22:59:51,535 - stpipe.Spec2Pipeline.extract_2d - INFO - Name of subarray extracted: 67
2022-12-03 22:59:51,536 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray x-extents are: 328 1789
2022-12-03 22:59:51,537 - stpipe.Spec2Pipeline.extract_2d - INFO - Subarray y-extents are: 131 150
2022-12-03 22:59:51,765 - stpipe.Spec2Pipeline.extract_2d - INFO - set slit_attributes completed
2022-12-03 22:59:51,774 - stpipe.Spec2Pipeline.extract_2d - INFO - Update S_REGION to POLYGON ICRS  156.158533940 -45.665758025 156.158408563 -45.665637125 156.158346784 -45.665669007 156.158472159 -45.665789909
2022-12-03 22:59:51,775 - stpipe.Spec2Pipeline.extract_2d - INFO - Updated S_REGION to POLYGON ICRS  156.158533940 -45.665758025 156.158408563 -45.665637125 156.158346784 -45.665669007 156.158472159 -45.665789909
2022-12-03 22:59:53,398 - stpipe.Spec2Pipeline.extract_2d - INFO - Step extract_2d done
2022-12-03 22:59:53,710 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:53,712 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'source_type': None}
2022-12-03 22:59:53,719 - stpipe.Spec2Pipeline.srctype - INFO - Input EXP_TYPE is NRS_MSASPEC
2022-12-03 22:59:53,720 - stpipe.Spec2Pipeline.srctype - INFO - source_id=53, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,722 - stpipe.Spec2Pipeline.srctype - INFO - source_id=54, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,723 - stpipe.Spec2Pipeline.srctype - INFO - source_id=42, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,725 - stpipe.Spec2Pipeline.srctype - INFO - source_id=43, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,726 - stpipe.Spec2Pipeline.srctype - INFO - source_id=44, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,727 - stpipe.Spec2Pipeline.srctype - INFO - source_id=45, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,728 - stpipe.Spec2Pipeline.srctype - INFO - source_id=46, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,730 - stpipe.Spec2Pipeline.srctype - INFO - source_id=47, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,731 - stpipe.Spec2Pipeline.srctype - INFO - source_id=48, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,732 - stpipe.Spec2Pipeline.srctype - INFO - source_id=49, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,733 - stpipe.Spec2Pipeline.srctype - INFO - source_id=50, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,734 - stpipe.Spec2Pipeline.srctype - INFO - source_id=51, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,735 - stpipe.Spec2Pipeline.srctype - INFO - source_id=52, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,736 - stpipe.Spec2Pipeline.srctype - INFO - source_id=55, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,737 - stpipe.Spec2Pipeline.srctype - INFO - source_id=65, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,739 - stpipe.Spec2Pipeline.srctype - INFO - source_id=66, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,740 - stpipe.Spec2Pipeline.srctype - INFO - source_id=68, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,741 - stpipe.Spec2Pipeline.srctype - INFO - source_id=56, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,742 - stpipe.Spec2Pipeline.srctype - INFO - source_id=57, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,743 - stpipe.Spec2Pipeline.srctype - INFO - source_id=58, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,744 - stpipe.Spec2Pipeline.srctype - INFO - source_id=59, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,745 - stpipe.Spec2Pipeline.srctype - INFO - source_id=60, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,746 - stpipe.Spec2Pipeline.srctype - INFO - source_id=61, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,747 - stpipe.Spec2Pipeline.srctype - INFO - source_id=62, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,749 - stpipe.Spec2Pipeline.srctype - INFO - source_id=63, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,750 - stpipe.Spec2Pipeline.srctype - INFO - source_id=64, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,751 - stpipe.Spec2Pipeline.srctype - INFO - source_id=67, stellarity=0.0000, type=EXTENDED
2022-12-03 22:59:53,753 - stpipe.Spec2Pipeline.srctype - INFO - Step srctype done
2022-12-03 22:59:54,054 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:54,060 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'force_subtract': False, 'save_background': False, 'user_background': None, 'inverse': False, 'steps': {'flat_field': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}, 'pathloss': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'barshadow': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'photom': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}}}
2022-12-03 22:59:54,068 - stpipe.Spec2Pipeline.master_background_mos - WARNING - No background slits available for creating master background. Skipping
2022-12-03 22:59:54,069 - stpipe.Spec2Pipeline.master_background_mos - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-03 22:59:54,069 - stpipe.Spec2Pipeline.master_background_mos - INFO - Step master_background_mos done
2022-12-03 22:59:54,357 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 22:59:54,358 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-03 22:59:57,112 - stpipe.Spec2Pipeline.wavecorr - INFO - Using WAVECORR reference file /grp/crds/cache/references/jwst/jwst_nirspec_wavecorr_0004.asdf
2022-12-03 23:00:02,080 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 53
2022-12-03 23:00:02,082 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 54
2022-12-03 23:00:02,082 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 42
2022-12-03 23:00:02,082 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 43
2022-12-03 23:00:02,083 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 44
2022-12-03 23:00:02,084 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 45
2022-12-03 23:00:02,084 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 46
2022-12-03 23:00:02,085 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 47
2022-12-03 23:00:02,086 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 48
2022-12-03 23:00:02,086 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 49
2022-12-03 23:00:02,086 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 50
2022-12-03 23:00:02,087 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 51
2022-12-03 23:00:02,087 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 52
2022-12-03 23:00:02,088 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 55
2022-12-03 23:00:02,088 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 65
2022-12-03 23:00:02,089 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 66
2022-12-03 23:00:02,089 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 68
2022-12-03 23:00:02,089 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 56
2022-12-03 23:00:02,090 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 57
2022-12-03 23:00:02,091 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 58
2022-12-03 23:00:02,091 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 59
2022-12-03 23:00:02,092 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 60
2022-12-03 23:00:02,093 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 61
2022-12-03 23:00:02,093 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 62
2022-12-03 23:00:02,094 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 63
2022-12-03 23:00:02,094 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 64
2022-12-03 23:00:02,095 - stpipe.Spec2Pipeline.wavecorr - INFO - Detected a EXTENDED source type in slit 67
2022-12-03 23:00:02,100 - stpipe.Spec2Pipeline.wavecorr - INFO - Step wavecorr done
2022-12-03 23:00:02,770 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 23:00:02,772 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': True, 'user_supplied_flat': None, 'inverse': False}
2022-12-03 23:00:32,662 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 53
2022-12-03 23:00:33,471 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 54
2022-12-03 23:00:34,276 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 42
2022-12-03 23:00:34,474 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 43
2022-12-03 23:00:34,732 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 44
2022-12-03 23:00:34,989 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 45
2022-12-03 23:00:35,328 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 46
2022-12-03 23:00:35,736 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 47
2022-12-03 23:00:36,184 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 48
2022-12-03 23:00:36,629 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 49
2022-12-03 23:00:37,129 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 50
2022-12-03 23:00:37,656 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 51
2022-12-03 23:00:38,182 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 52
2022-12-03 23:00:38,759 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 55
2022-12-03 23:00:40,310 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 65
2022-12-03 23:00:42,486 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 66
2022-12-03 23:00:45,072 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 68
2022-12-03 23:00:47,260 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 56
2022-12-03 23:00:49,003 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 57
2022-12-03 23:00:50,883 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 58
2022-12-03 23:00:52,845 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 59
2022-12-03 23:00:54,892 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 60
2022-12-03 23:00:56,985 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 61
2022-12-03 23:00:59,100 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 62
2022-12-03 23:01:01,255 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 63
2022-12-03 23:01:03,287 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 64
2022-12-03 23:01:05,431 - stpipe.Spec2Pipeline.flat_field - INFO - Working on slit 67
2022-12-03 23:01:15,984 - stpipe.Spec2Pipeline.flat_field - INFO - Saved model in mos_g140m_line1_NRS1_interpolatedflat.fits
2022-12-03 23:01:15,985 - stpipe.Spec2Pipeline.flat_field - INFO - Interpolated flat written to "mos_g140m_line1_NRS1_interpolatedflat.fits".
2022-12-03 23:01:15,992 - stpipe.Spec2Pipeline.flat_field - INFO - Step flat_field done
2022-12-03 23:01:16,553 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 23:01:16,555 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-12-03 23:01:16,556 - stpipe.Spec2Pipeline.pathloss - INFO - Step skipped.
2022-12-03 23:01:16,559 - stpipe.Spec2Pipeline.pathloss - INFO - Step pathloss done
2022-12-03 23:01:16,925 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 23:01:16,927 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-12-03 23:01:16,927 - stpipe.Spec2Pipeline.barshadow - INFO - Step skipped.
2022-12-03 23:01:16,930 - stpipe.Spec2Pipeline.barshadow - INFO - Step barshadow done
2022-12-03 23:01:17,253 - stpipe.Spec2Pipeline.photom - INFO - Step photom running with args (<MultiSlitModel from mos_g140m_line1_NRS1_uncal.fits>,).
2022-12-03 23:01:17,254 - stpipe.Spec2Pipeline.photom - INFO - Step photom parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-12-03 23:01:17,255 - stpipe.Spec2Pipeline.photom - INFO - Step skipped.
2022-12-03 23:01:17,257 - stpipe.Spec2Pipeline.photom - INFO - Step photom done
2022-12-03 23:01:17,581 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec running with args (<MultiSlitModel from mos_g140m_line1_NRS1_cal.fits>,).
2022-12-03 23:01:17,583 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': 's2d', 'search_output_file': True, 'input_dir': '', 'pixfrac': 1.0, 'kernel': 'square', 'fillval': 'INDEF', 'weight_type': 'ivm', 'output_shape': None, 'crpix': None, 'crval': None, 'rotation': None, 'pixel_scale_ratio': 1.0, 'pixel_scale': None, 'single': False, 'blendheaders': True, 'allowed_memory': None, 'in_memory': True}
2022-12-03 23:01:17,583 - stpipe.Spec2Pipeline.resample_spec - INFO - Step skipped.
2022-12-03 23:01:17,586 - stpipe.Spec2Pipeline.resample_spec - INFO - Step resample_spec done
2022-12-03 23:01:17,869 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d running with args (<MultiSlitModel from mos_g140m_line1_NRS1_cal.fits>,).
2022-12-03 23:01:17,871 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': 'x1d', 'search_output_file': True, 'input_dir': '', 'smoothing_length': None, 'bkg_fit': None, 'bkg_order': None, 'bkg_sigma_clip': 3.0, 'log_increment': 50, 'subtract_background': None, 'use_source_posn': None, 'center_xy': None, 'apply_apcorr': True, 'soss_threshold': 0.01, 'soss_n_os': 2, 'soss_transform': None, 'soss_tikfac': None, 'soss_width': 40.0, 'soss_bad_pix': 'model', 'soss_modelname': None}
2022-12-03 23:01:17,871 - stpipe.Spec2Pipeline.extract_1d - INFO - Step skipped.
2022-12-03 23:01:17,874 - stpipe.Spec2Pipeline.extract_1d - INFO - Step extract_1d done
2022-12-03 23:01:17,875 - stpipe.Spec2Pipeline - INFO - Finished processing product mos_g140m_line1_NRS1_uncal
2022-12-03 23:01:17,875 - stpipe.Spec2Pipeline - INFO - Ending calwebb_spec2
2022-12-03 23:01:17,875 - stpipe.Spec2Pipeline - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-03 23:01:17,876 - stpipe.Spec2Pipeline - INFO - Step Spec2Pipeline done

Running flat field test for MOS...
Filename: mos_g140m_line1_NRS1_interpolatedflat.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU     268   ()      
  1  SCI           1 ImageHDU        14   (506, 10)   float32   
  2  DQ            1 ImageHDU        11   (506, 10)   int32 (rescales to uint32)   
  3  ERR           1 ImageHDU         9   (506, 10)   float32   
  4  WAVELENGTH    1 ImageHDU         9   (506, 10)   float32   
  5  SCI           2 ImageHDU        14   (506, 10)   float32   
  6  DQ            2 ImageHDU        11   (506, 10)   int32 (rescales to uint32)   
  7  ERR           2 ImageHDU         9   (506, 10)   float32   
  8  WAVELENGTH    2 ImageHDU         9   (506, 10)   float32   
  9  SCI           3 ImageHDU        14   (30, 9)   float32   
 10  DQ            3 ImageHDU        11   (30, 9)   int32 (rescales to uint32)   
 11  ERR           3 ImageHDU         9   (30, 9)   float32   
 12  WAVELENGTH    3 ImageHDU         9   (30, 9)   float32   
 13  SCI           4 ImageHDU        14   (78, 9)   float32   
 14  DQ            4 ImageHDU        11   (78, 9)   int32 (rescales to uint32)   
 15  ERR           4 ImageHDU         9   (78, 9)   float32   
 16  WAVELENGTH    4 ImageHDU         9   (78, 9)   float32   
 17  SCI           5 ImageHDU        14   (79, 9)   float32   
 18  DQ            5 ImageHDU        11   (79, 9)   int32 (rescales to uint32)   
 19  ERR           5 ImageHDU         9   (79, 9)   float32   
 20  WAVELENGTH    5 ImageHDU         9   (79, 9)   float32   
 21  SCI           6 ImageHDU        14   (140, 10)   float32   
 22  DQ            6 ImageHDU        11   (140, 10)   int32 (rescales to uint32)   
 23  ERR           6 ImageHDU         9   (140, 10)   float32   
 24  WAVELENGTH    6 ImageHDU         9   (140, 10)   float32   
 25  SCI           7 ImageHDU        14   (166, 10)   float32   
 26  DQ            7 ImageHDU        11   (166, 10)   int32 (rescales to uint32)   
 27  ERR           7 ImageHDU         9   (166, 10)   float32   
 28  WAVELENGTH    7 ImageHDU         9   (166, 10)   float32   
 29  SCI           8 ImageHDU        14   (233, 9)   float32   
 30  DQ            8 ImageHDU        11   (233, 9)   int32 (rescales to uint32)   
 31  ERR           8 ImageHDU         9   (233, 9)   float32   
 32  WAVELENGTH    8 ImageHDU         9   (233, 9)   float32   
 33  SCI           9 ImageHDU        14   (233, 9)   float32   
 34  DQ            9 ImageHDU        11   (233, 9)   int32 (rescales to uint32)   
 35  ERR           9 ImageHDU         9   (233, 9)   float32   
 36  WAVELENGTH    9 ImageHDU         9   (233, 9)   float32   
 37  SCI          10 ImageHDU        14   (257, 10)   float32   
 38  DQ           10 ImageHDU        11   (257, 10)   int32 (rescales to uint32)   
 39  ERR          10 ImageHDU         9   (257, 10)   float32   
 40  WAVELENGTH   10 ImageHDU         9   (257, 10)   float32   
 41  SCI          11 ImageHDU        14   (274, 10)   float32   
 42  DQ           11 ImageHDU        11   (274, 10)   int32 (rescales to uint32)   
 43  ERR          11 ImageHDU         9   (274, 10)   float32   
 44  WAVELENGTH   11 ImageHDU         9   (274, 10)   float32   
 45  SCI          12 ImageHDU        14   (289, 10)   float32   
 46  DQ           12 ImageHDU        11   (289, 10)   int32 (rescales to uint32)   
 47  ERR          12 ImageHDU         9   (289, 10)   float32   
 48  WAVELENGTH   12 ImageHDU         9   (289, 10)   float32   
 49  SCI          13 ImageHDU        14   (326, 10)   float32   
 50  DQ           13 ImageHDU        11   (326, 10)   int32 (rescales to uint32)   
 51  ERR          13 ImageHDU         9   (326, 10)   float32   
 52  WAVELENGTH   13 ImageHDU         9   (326, 10)   float32   
 53  SCI          14 ImageHDU        14   (1026, 14)   float32   
 54  DQ           14 ImageHDU        11   (1026, 14)   int32 (rescales to uint32)   
 55  ERR          14 ImageHDU         9   (1026, 14)   float32   
 56  WAVELENGTH   14 ImageHDU         9   (1026, 14)   float32   
 57  SCI          15 ImageHDU        14   (1466, 21)   float32   
 58  DQ           15 ImageHDU        11   (1466, 21)   int32 (rescales to uint32)   
 59  ERR          15 ImageHDU         9   (1466, 21)   float32   
 60  WAVELENGTH   15 ImageHDU         9   (1466, 21)   float32   
 61  SCI          16 ImageHDU        14   (1466, 21)   float32   
 62  DQ           16 ImageHDU        11   (1466, 21)   int32 (rescales to uint32)   
 63  ERR          16 ImageHDU         9   (1466, 21)   float32   
 64  WAVELENGTH   16 ImageHDU         9   (1466, 21)   float32   
 65  SCI          17 ImageHDU        14   (1467, 23)   float32   
 66  DQ           17 ImageHDU        11   (1467, 23)   int32 (rescales to uint32)   
 67  ERR          17 ImageHDU         9   (1467, 23)   float32   
 68  WAVELENGTH   17 ImageHDU         9   (1467, 23)   float32   
 69  SCI          18 ImageHDU        14   (1176, 14)   float32   
 70  DQ           18 ImageHDU        11   (1176, 14)   int32 (rescales to uint32)   
 71  ERR          18 ImageHDU         9   (1176, 14)   float32   
 72  WAVELENGTH   18 ImageHDU         9   (1176, 14)   float32   
 73  SCI          19 ImageHDU        14   (1243, 15)   float32   
 74  DQ           19 ImageHDU        11   (1243, 15)   int32 (rescales to uint32)   
 75  ERR          19 ImageHDU         9   (1243, 15)   float32   
 76  WAVELENGTH   19 ImageHDU         9   (1243, 15)   float32   
 77  SCI          20 ImageHDU        14   (1317, 16)   float32   
 78  DQ           20 ImageHDU        11   (1317, 16)   int32 (rescales to uint32)   
 79  ERR          20 ImageHDU         9   (1317, 16)   float32   
 80  WAVELENGTH   20 ImageHDU         9   (1317, 16)   float32   
 81  SCI          21 ImageHDU        14   (1390, 16)   float32   
 82  DQ           21 ImageHDU        11   (1390, 16)   int32 (rescales to uint32)   
 83  ERR          21 ImageHDU         9   (1390, 16)   float32   
 84  WAVELENGTH   21 ImageHDU         9   (1390, 16)   float32   
 85  SCI          22 ImageHDU        14   (1407, 17)   float32   
 86  DQ           22 ImageHDU        11   (1407, 17)   int32 (rescales to uint32)   
 87  ERR          22 ImageHDU         9   (1407, 17)   float32   
 88  WAVELENGTH   22 ImageHDU         9   (1407, 17)   float32   
 89  SCI          23 ImageHDU        14   (1428, 17)   float32   
 90  DQ           23 ImageHDU        11   (1428, 17)   int32 (rescales to uint32)   
 91  ERR          23 ImageHDU         9   (1428, 17)   float32   
 92  WAVELENGTH   23 ImageHDU         9   (1428, 17)   float32   
 93  SCI          24 ImageHDU        14   (1462, 18)   float32   
 94  DQ           24 ImageHDU        11   (1462, 18)   int32 (rescales to uint32)   
 95  ERR          24 ImageHDU         9   (1462, 18)   float32   
 96  WAVELENGTH   24 ImageHDU         9   (1462, 18)   float32   
 97  SCI          25 ImageHDU        14   (1461, 18)   float32   
 98  DQ           25 ImageHDU        11   (1461, 18)   int32 (rescales to uint32)   
 99  ERR          25 ImageHDU         9   (1461, 18)   float32   
100  WAVELENGTH   25 ImageHDU         9   (1461, 18)   float32   
101  SCI          26 ImageHDU        14   (1461, 18)   float32   
102  DQ           26 ImageHDU        11   (1461, 18)   int32 (rescales to uint32)   
103  ERR          26 ImageHDU         9   (1461, 18)   float32   
104  WAVELENGTH   26 ImageHDU         9   (1461, 18)   float32   
105  SCI          27 ImageHDU        14   (1461, 19)   float32   
106  DQ           27 ImageHDU        11   (1461, 19)   int32 (rescales to uint32)   
107  ERR          27 ImageHDU         9   (1461, 19)   float32   
108  WAVELENGTH   27 ImageHDU         9   (1461, 19)   float32   
109  ASDF          1 BinTableHDU     11   1R x 1C   [2262015B]   
flat_field_file  -->     Grating:G140M   Filter:F100LP   LAMP:LINE1
Using D-flat: /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04/nirspec_dflat_nrs1_f_01.03.fits
Using S-flat: /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04/nirspec_MOS_sflat_G140M_OPAQUE_FLAT1_nrs1_f_01.01.fits
Using F-flat: /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpc4g9b_04/nirspec_MOS_fflat_F100LP_01.01.fits

Working with slit ID: 53 - which is 1 out of 27
 Subwindow origin:   px0=1543   py0=1317
silt_id='53'   quad=1   row=330   col=144   slitlet_id='330_144'
Now looping through the pixels, this will take a while ... 
Calculating statistics... 

   Absolute Flat Difference  :   mean = -5.786e-07    median = 1.294e-07    stdev = 2.252e-04
    Maximum   AbsoluteFlat Difference = 1.124e-03
    Minimum   AbsoluteFlat Difference = -1.066e-03
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 56%
                            ->  3xtheshold = 15%
                            ->  5xtheshold = 4%

 *** WARNING: More than 10% of pixels have a median value greater than 3xthreshold!

Making histogram plot for this slitlet...

 *** Result of the test: PASSED


Working with slit ID: 54 - which is 2 out of 27
 Subwindow origin:   px0=1543   py0=1307
silt_id='54'   quad=1   row=330   col=146   slitlet_id='330_146'
Now looping through the pixels, this will take a while ... 
Calculating statistics... 

   Absolute Flat Difference  :   mean = -5.342e-06    median = -9.358e-07    stdev = 2.279e-04
    Maximum   AbsoluteFlat Difference = 1.021e-03
    Minimum   AbsoluteFlat Difference = -1.173e-03
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 56%
                            ->  3xtheshold = 16%
                            ->  5xtheshold = 4%

 *** WARNING: More than 10% of pixels have a median value greater than 3xthreshold!

Making histogram plot for this slitlet...

 *** Result of the test: PASSED


Working with slit ID: 42 - which is 3 out of 27
 Subwindow origin:   px0=2019   py0=547
silt_id='42'   quad=2   row=138   col=56   slitlet_id='138_56'
Now looping through the pixels, this will take a while ... 
Calculating statistics... 
 * Unable to calculate statistics because difference array has all outlier values.
   Test will be set to FAILED and NO plots will be made.
 *** Result of the test: FAILED


Working with slit ID: 43 - which is 4 out of 27
 Subwindow origin:   px0=1971   py0=416
silt_id='43'   quad=2   row=155   col=82   slitlet_id='155_82'
Now looping through the pixels, this will take a while ...

/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/flattest_mos.py:534: RuntimeWarning: invalid value encountered in divide
  sff = int_tab/(last_sfv_wav - first_sfv_wav)

Calculating statistics... 

   Absolute Flat Difference  :   mean = 5.415e-05    median = 6.258e-05    stdev = 3.413e-04
    Maximum   AbsoluteFlat Difference = 9.230e-04
    Minimum   AbsoluteFlat Difference = -7.970e-04
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 81%
                            ->  3xtheshold = 37%
                            ->  5xtheshold = 16%

 *** WARNING: More than 10% of pixels have a median value greater than 3xthreshold!


 *** WARNING: More than 10% of pixels have a median value greater than 5xthreshold!

Making histogram plot for this slitlet...

 *** Result of the test: PASSED


Working with slit ID: 44 - which is 5 out of 27
 Subwindow origin:   px0=1970   py0=406
silt_id='44'   quad=2   row=155   col=84   slitlet_id='155_84'
Now looping through the pixels, this will take a while ... 
Calculating statistics... 

   Absolute Flat Difference  :   mean = 5.742e-06    median = 1.744e-05    stdev = 3.107e-04
    Maximum   AbsoluteFlat Difference = 8.052e-04
    Minimum   AbsoluteFlat Difference = -7.523e-04
    Percentage of pixels where median of absolute differences is greater than: 
                            ->  1xtheshold = 76%
                            ->  3xtheshold = 31%
                            ->  5xtheshold = 11%

 *** WARNING: More than 10% of pixels have a median value greater than 3xthreshold!


 *** WARNING: More than 10% of pixels have a median value greater than 5xthreshold!

Making histogram plot for this slitlet...


# Quickly see if the test passed 

print('These are the final results of the tests: ')
for key, val in results_dict.items():
    if not isinstance(val, str):
        if val:
            val = 'PASSED'
        else:
            val = 'FAILED'
    print('{:<42} {:<8}'.format(key, val))

These are the final results of the tests: 
mos_g140m_line1_NRS1_uncal.fits            FAILED  
mos_g140m_line1_NRS2_uncal.fits            PASSED

JWST Pipeline Validation Testing Notebook: spec2, flat_field step for mos¶

Table of Contents¶

Imports¶

Test Description¶

Test Results¶

Calibration WG Requested Algorithm:¶

Defining Term¶

Run the JWST pipeline and assign_wcs validation tests¶

Testing Data Set¶

About this Notebook¶